Background: The relationship between the quality of the physician-patient relationship and the outcomes of the clinical encounters in primary care are examined. Method: Focus groups of physicians and patients. A total of 24 professionals and 22 patients took part. Results: The physicians perceived a relationship to exist between the scarcity of healthcare resources (short length of time with each patient, care-providing overload, lack of specific resources, lack of training), conflicts with "difficult" patients and the influence of the psychosocial factors in the clinical encounter and error, burnout, defensive medicine and the low quality of the services. Communication/examination-related problems during the clinical interview and by negative feelings acted as intermediary factors in this relationship. The patients perceived a relationship to exist between an operating pattern characterized by short office visits scheduled at an overloaded pace and physician, patient communications problems and error and conflict in the clinical encounter. There is also a relationship between the physician's humanist attitude and a better outcome of the health problems. The objectives and priorities of the health care system, out of touch with the needs of the community, are seen as being key determining factors as regards the lacks considered to exist. Conclusions:. The physician-patient relationship processes play a mediating role between the health care resources and the outcomes of the clinical encounters. Improving the care provided and the physician-patient relationship in primary care requires a multi-dimensional approach and view which goes beyond the measures taken regarding individual physician and patient-related factors.